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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ), 'gf_id' => 'HOM05D001647', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001647' ), 'data_identifier' => 'HOM05D001647', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001647', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '393', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35540' => 'bna', 'A03p26360' => 'bna', 'A06p41080' => 'bna', 'A07p06950' => 'bna', 'A07p19040' => 'bna', 'A08p07170' => 'bna', 'Aa31LG10G910' => 'aar', 'Aa31LG2G5110' => 'aar', 'Aa31LG5G22420' => 'aar', 'Aa31sc53G80' => 'aar', 'Actinidia05984' => 'ach', 'Actinidia05985' => 'ach', 'Actinidia30004' => 'ach', 'Actinidia34598' => 'ach', 'Actinidia34599' => 'ach', 'Actinidia36122' => 'ach', 'Ah.01g006080' => 'amhyb', 'Ah.01g007510' => 'amhyb', 'Ah.07g202130' => 'amhyb', 'Ah.09g232790' => 'amhyb', 'AL4G21530' => 'aly', 'AL5G16970' => 'aly', 'AL9U11200' => 'aly', 'Aqoxy102s003' => 'aox', 'Aqoxy2G00647' => 'aox', 'Aqoxy5G02538' => 'aox', 'Aqoxy5G03747' => 'aox', 'Aqoxy6G01579' => 'aox', 'Aqoxy6G01580' => 'aox', 'Aqoxy6G01582' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Q1I8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BA4K4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4MAIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UJPA' => 'arhy', 'AT2G28480' => 'ath', 'AT3G25440' => 'ath', 'AT3G27550' => 'ath', 'AT4G13070' => 'ath', 'ATR0743G047' => 'atr', 'ATR0824G238' => 'atr', 'ATR0824G265' => 'atr', 'Atru.BG.203.p' => 'acertr', 'Atru.chr4.2956' => 'acertr', 'Atru.chr6.2421' => 'acertr', 'Atru.chr6.3532' => 'acertr', 'Atru.chr8.762' => 'acertr', 'AUR62002323' => 'cqu', 'AUR62003265' => 'cqu', 'AUR62010426' => 'cqu', 'AUR62016795' => 'cqu', 'AUR62023863' => 'cqu', 'AUR62027203' => 'cqu', 'BcaB01g03105' => 'bca', 'BcaB02g10162' => 'bca', 'BcaB04g17720' => 'bca', 'BcaB06g26746' => 'bca', 'BcaB07g30153' => 'bca', 'BcaC01g04968' => 'bca', 'BcaC03g17472' => 'bca', 'BcaC04g23899' => 'bca', 'BcaC06g30978' => 'bca', 'BcaC06g33804' => 'bca', 'BolC2t11499H' => 'bol', 'BolC3t15505H' => 'bol', 'BolC4t23784H' => 'bol', 'BolC8t47723H' => 'bol', 'BolC9t53286H' => 'bol', 'BraA02t08556Z' => 'bra', 'BraA06t27031Z' => 'bra', 'BraA07t28485Z' => 'bra', 'BraA08t32729Z' => 'bra', 'C03p31620' => 'bna', 'C04p22880' => 'bna', 'C07p36660' => 'bna', 'C08p08760' => 'bna', 'C09p03660' => 'bna', 'CAN.G1002.19' => 'can', 'CAN.G292.10' => 'can', 'CAN.G404.63' => 'can', 'CAN.G523.79' => 'can', 'CAN.G874.36' => 'can', 'CANSAT01G2191' => 'cansat', 'CANSAT35G0730' => 'cansat', 'CANSAT64G2892' => 'cansat', 'CARHR121430' => 'chi', 'CARHR148920' => 'chi', 'CARHR148930' => 'chi', 'CARHR218470' => 'chi', 'Carub.0004s0942' => 'cru', 'Carub.0005s0598' => 'cru', 'Carub.0007s2969' => 'cru', 'Ca_00794_v3' => 'car', 'Ca_04144_v3' => 'car', 'Ca_11741_v3' => 'car', 'Ca_20792_v3' => 'car', 'Cc01_g16000' => 'ccan', 'Cc03_g11950' => 'ccan', 'Cc03_g12350' => 'ccan', 'Cc03_g12360' => 'ccan', 'Cc03_g14500' => 'ccan', 'Cc04_g16720' => 'ccan', 'Cc07_g01540' => 'ccan', 'CDE02G4217' => 'cde', 'CDE03G0001' => 'cde', 'CDE10G0781' => 'cde', 'CDE10G1164' => 'cde', 'Cfa005613' => 'cfa', 'Cfa015176' => 'cfa', 'Ciclev10014676m.g' => 'ccl', 'Ciclev10017344m.g' => 'ccl', 'Ciclev10020228m.g' => 'ccl', 'Ciclev10030211m.g' => 'ccl', 'CiPaw.02G054100' => 'cil', 'CiPaw.05G037000' => 'cil', 'CiPaw.05G037300' => 'cil', 'ClCG08G010700' => 'cla', 'ClCG09G015320' => 'cla', 'ClCG09G019350' => 'cla', 'ClCG10G015540' => 'cla', 'COL.COLO4_08155' => 'col', 'COL.COLO4_16174' => 'col', 'COL.COLO4_32812' => 'col', 'Cpa.g.c39129' => 'cpa', 'Cpa.g.sc2900.3' => 'cpa', 'Cpa.g.sc9.296' => 'cpa', 'CsaV3_3G040890' => 'csa', 'CsaV3_5G027060' => 'csa', 'CsaV3_7G006390' => 'csa', 'CSS0005156' => 'camsi', 'CSS0009907' => 'camsi', 'CSS0014342' => 'camsi', 'CSS0025040' => 'camsi', 'CSS0028879' => 'camsi', 'CSS0031246' => 'camsi', 'CSS0041249' => 'camsi', 'CSS0045042' => 'camsi', 'CSS0046209' => 'camsi', 'CSS0049659' => 'camsi', 'DCAR_001173' => 'dca', 'DCAR_004772' => 'dca', 'DCAR_009853' => 'dca', 'DCAR_021853' => 'dca', 'Dinv22746' => 'din', 'Dinv28803' => 'din', 'Dinv33429' => 'din', 'Duzib132G0204' => 'dzi', 'Duzib138G0715' => 'dzi', 'Duzib147G0348' => 'dzi', 'Duzib212G0802' => 'dzi', 'ECA246G2376' => 'eca', 'ECA248G3096' => 'eca', 'ECA248G3160' => 'eca', 'EL10Ac3g05979' => 'bvu', 'EL10Ac6g14819' => 'bvu', 'EL10Ac9g21220' => 'bvu', 'EL10Ac9g21672' => 'bvu', 'Eucgr.A00093' => 'egr', 'Eucgr.I01734' => 'egr', 'Eucgr.I02671' => 'egr', 'FAN02G3474' => 'fan', 'FAN05G1297' => 'fan', 'FAN07G0844' => 'fan', 'FAN09G0821' => 'fan', 'FAN12G2494' => 'fan', 'FAN14G0654' => 'fan', 'FAN14G0999' => 'fan', 'FAN17G2196' => 'fan', 'FAN19G1664' => 'fan', 'FAN23G1587' => 'fan', 'FAN26G2350' => 'fan', 'FvH4_1g30180' => 'fve', 'FvH4_4g10890' => 'fve', 'FvH4_6g51690' => 'fve', 'Glyma.05G002800' => 'gma', 'Glyma.05G236500' => 'gma', 'Glyma.08G043700' => 'gma', 'Glyma.11G127300' => 'gma', 'Glyma.12G051900' => 'gma', 'Glyma.19G003000' => 'gma', 'Gohir.A05G355000' => 'ghi', 'Gohir.A09G211500' => 'ghi', 'Gohir.A13G066300' => 'ghi', 'Gohir.D04G058200' => 'ghi', 'Gohir.D09G205000' => 'ghi', 'Gohir.D11G149700' => 'ghi', 'Gohir.D11G235100' => 'ghi', 'Gohir.D13G055200' => 'ghi', 'Gorai.006G229000' => 'gra', 'Gorai.007G247800' => 'gra', 'Gorai.012G064900' => 'gra', 'Gorai.013G062300' => 'gra', 'GSVIVG01010789001' => 'vvi', 'GSVIVG01032387001' => 'vvi', 'GSVIVG01037932001' => 'vvi', 'HanXRQChr01g0023811' => 'han', 'HanXRQChr01g0025091' => 'han', 'HanXRQChr16g0514011' => 'han', 'HanXRQChr17g0548611' => 'han', 'Haze_03579' => 'cav', 'Haze_10656' => 'cav', 'Hma1.2p1_0704F.1_g206740' => 'hma', 'Hma1.2p1_1747F.1_g300520' => 'hma', 'HPP92_000950' => 'vpl', 'HPP92_000962' => 'vpl', 'HPP92_000963' => 'vpl', 'HPP92_018918' => 'vpl', 'HPP92_023713' => 'vpl', 'Hund03168' => 'sun', 'Lalb_Chr03g0026081' => 'lal', 'Lalb_Chr11g0068561' => 'lal', 'Lalb_Chr16g0387771' => 'lal', 'Lj1A103T30' => 'lonja', 'Lj2g0023354' => 'lja', 'Lj3A10G10' => 'lonja', 'Lj3A23G21' => 'lonja', 'Lj3g0005963' => 'lja', 'Lj4g0011979' => 'lja', 'Lj6A11T15' => 'lonja', 'Lj6C11T4' => 'lonja', 'Lj7A600G51' => 'lonja', 'Lj9A354G35' => 'lonja', 'Lsat_1_v5_gn_0_47341' => 'lsa', 'Lsat_1_v5_gn_1_77501' => 'lsa', 'Lsat_1_v5_gn_5_107120' => 'lsa', 'Lsat_1_v5_gn_5_176681' => 'lsa', 'Manes.04G043600' => 'mes', 'Manes.15G151600' => 'mes', 'Manes.17G115300' => 'mes', 'MBI08_g20601_MAGBIO' => 'mbi', 'MBI15_g42001_MAGBIO' => 'mbi', 'MBI16_g05784_MAGBIO' => 'mbi', 'MD04G1042300' => 'mdo', 'MD09G1023500' => 'mdo', 'MD10G1049100' => 'mdo', 'MD10G1150100' => 'mdo', 'MD10G1150200' => 'mdo', 'MD10G1150300' => 'mdo', 'MD13G1272400' => 'mdo', 'MD17G1023000' => 'mdo', 'Medtr1g050760' => 'mtr', 'Medtr4g067300' => 'mtr', 'Medtr4g120880' => 'mtr', 'Medtr6g004480' => 'mtr', 'Medtr8g104790' => 'mtr', 'MELO3C009824.2' => 'cme', 'MELO3C018653.2' => 'cme', 'MELO3C021588.2' => 'cme', 'Migut.B00618' => 'egut', 'Migut.D01562' => 'egut', 'Migut.H00066' => 'egut', 'MSTRG.20299' => 'ama', 'MSTRG.27406' => 'ama', 'MSTRG.3140' => 'ama', 'Nitab4.5_0000038g0290' => 'nta', 'Nitab4.5_0000065g0270' => 'nta', 'Nitab4.5_0000335g0080' => 'nta', 'Nitab4.5_0000489g0100' => 'nta', 'Nitab4.5_0000489g0110' => 'nta', 'Nitab4.5_0000511g0050' => 'nta', 'Nitab4.5_0002077g0020' => 'nta', 'Nitab4.5_0003174g0020' => 'nta', 'Nitab4.5_0003267g0020' => 'nta', 'Nitab4.5_0003858g0030' => 'nta', 'Nitab4.5_0006002g0030' => 'nta', 'Nn1g09609' => 'nnu', 'Nn3g16694' => 'nnu', 'Nn3g17239' => 'nnu', 'Nn8g39866' => 'nnu', 'Oeu000238.1' => 'oeu', 'Oeu032634.1' => 'oeu', 'Oeu039462.1' => 'oeu', 'Oeu053823.2' => 'oeu', 'Oeu054628.1' => 'oeu', 'Os01g0958400' => 'osa', 'Os05g0145300' => 'osa', 'Os06g0304500' => 'osa', 'Peaxi162Scf00001g00221' => 'pax', 'Peaxi162Scf00141g00924' => 'pax', 'Peaxi162Scf00672g00011' => 'pax', 'Peaxi162Scf00700g00436' => 'pax', 'Peaxi162Scf01242g00039' => 'pax', 'PGR083G0602' => 'pgr', 'PGR142G1579' => 'pgr', 'PGR142G3896' => 'pgr', 'PGSC0003DMG400006153' => 'stu', 'PGSC0003DMG400011786' => 'stu', 'PGSC0003DMG400012587' => 'stu', 'PGSC0003DMG400015335' => 'stu', 'PGSC0003DMG401027685' => 'stu', 'Phvul.004G005000' => 'pvu', 'Phvul.008G012400' => 'pvu', 'Phvul.011G053900' => 'pvu', 'Potri.001G343700' => 'ptr', 'Potri.007G129600' => 'ptr', 'Potri.013G083000' => 'ptr', 'Prupe.1G196500' => 'ppe', 'Prupe.3G293300' => 'ppe', 'Prupe.7G001900' => 'ppe', 'Psat1g053800' => 'psa', 'Psat6g093440' => 'psa', 'Psat7g009000' => 'psa', 'Psat7g115160' => 'psa', 'Psat7g209920' => 'psa', 'PSO063G0624' => 'pso', 'PSO067G0082' => 'pso', 'QL01p055435' => 'qlo', 'QL01p055440' => 'qlo', 'QL02p074109' => 'qlo', 'QL05p019466' => 'qlo', 'QL09p047372' => 'qlo', 'QL10p050116' => 'qlo', 'QL11p020509' => 'qlo', 'RcHm_v2.0_Chr2g0173221' => 'rch', 'RcHm_v2.0_Chr3g0491551' => 'rch', 'RcHm_v2.0_Chr4g0406531' => 'rch', 'Rhsim02G0081300' => 'rsi', 'Rhsim11G0136100' => 'rsi', 'Sabra06G0126000' => 'sbr', 'Sabra07G0105500' => 'sbr', 'Sabra13G0071800' => 'sbr', 'Sabra14G0135200' => 'sbr', 'Sabra16G0223000' => 'sbr', 'SalBow1G0849' => 'sbo', 'SalBow3G2773' => 'sbo', 'SalBow3G2902' => 'sbo', 'SalBow4G1893' => 'sbo', 'SalBow5G2767' => 'sbo', 'SalBow5G4276' => 'sbo', 'SalBow7G2325' => 'sbo', 'SalBow7G2333' => 'sbo', 'Sc06g0002120' => 'sci', 'Sc18g0005250' => 'sci', 'Sc19g0002950' => 'sci', 'Sed0000147' => 'sed', 'Sed0028231' => 'sed', 'SEGI_12464' => 'sgi', 'SEGI_32949' => 'sgi', 'SEGI_39124' => 'sgi', 'SGA_v2.0_scaffold221G42702' => 'sas', 'SGA_v2.0_scaffold28G11975' => 'sas', 'SGA_v2.0_scaffold2G01173' => 'sas', 'SGA_v2.0_scaffold42G16007' => 'sas', 'SHI16456' => 'shi', 'Solyc01g105090.3' => 'sly', 'Solyc06g082990.4' => 'sly', 'Solyc07g047900.3' => 'sly', 'Solyc09g005270.3' => 'sly', 'Solyc12g014280.2' => 'sly', 'Sopen01g047630' => 'spe', 'Sopen06g034380' => 'spe', 'Sopen07g024330' => 'spe', 'Sopen09g001240' => 'spe', 'Sopen12g006070' => 'spe', 'Sp2g16720' => 'spa', 'Sp3g22980' => 'spa', 'Sp4g11300' => 'spa', 'Sp7g10330' => 'spa', 'TAR622G0864' => 'tar', 'TAR633G0142' => 'tar', 'TAR633G0372' => 'tar', 'THA.LOC104804621' => 'tha', 'THA.LOC104815857' => 'tha', 'THA.LOC104823954' => 'tha', 'Thecc.01G209400' => 'tca', 'Thecc.02G140600' => 'tca', 'Thecc.04G019000' => 'tca', 'Thecc.04G177300' => 'tca', 'Thhalv10004117m.g' => 'esa', 'Thhalv10016829m.g' => 'esa', 'TPR.G31951' => 'tpr', 'TPR.G32700' => 'tpr', 'TPR.G34241' => 'tpr', 'TPR.G7602' => 'tpr', 'TWI15G0581' => 'twi', 'TWI36G0803' => 'twi', 'TWI56G0370' => 'twi', 'TWI59G0229' => 'twi', 'unitig_37.g12021' => 'ugi', 'unitig_52.g17659' => 'ugi', 'unitig_61.g26346' => 'ugi', 'unitig_61.g26347' => 'ugi', 'vmacro01820' => 'vma', 'vmacro05874' => 'vma', 'VMungo0464G0398' => 'vmu', 'VMungo1127G0433' => 'vmu', 'VMungo1127G2188' => 'vmu', 'VMungo1383G0270' => 'vmu', 'VMungo1383G1972' => 'vmu', 'VMungo1383G2159' => 'vmu', 'Zm00001eb140480' => 'zma', 'Zm00001eb354360' => 'zma', 'Zm00001eb417950' => 'zma', 'Zm00001eb425090' => 'zma' ) $gf_id = 'HOM05D001647' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001647' ) $data_identifier = 'HOM05D001647' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 3, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425090' $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